The court announced the indictment on Friday, Swedish Television reports. Maru could not attend the hearing due to health reasons, but staff from the Swedish Embassy was present.
The charges stem from a fire at his prison that killed dozens of inmates in September. The details surrounding the fire are unclear but Swedish Television previously reported that Ethiopian authorities have charged some 38 prisoners in court for causing the deadly blaze.
Maru's daughter, Emy Maru, was not at the hearing but had the indictment read back to her.
"The prosecutor says that dad was the ringleader behind the rebellion and the fire that broke out at the jail the day after he was taken to hospital. He's said to be the one who financed the riot from the hospital he started here in Addis Ababa," she told Swedish Television.
Maru was arrested in May 2013 in Addis Ababa as he was overseeing the construction of a hospital he established. He was originally apprehended for allegedly smuggling medical supplies into the country. The charges were later dropped before he was eventually arrested for having knowledge of corruption between a minister and a prosecutor. Maru has always denied any wrongdoing.